From 780e01787179c4515c1e7f1857136cb8bf4545cd Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Fri, 20 Sep 2024 10:15:26 +0200
Subject: [PATCH] Roughed in more bounding box generator
---
model_server/base/roiset.py | 19 ++++++++++++++-----
tests/base/test_roiset.py | 8 ++++++++
2 files changed, 22 insertions(+), 5 deletions(-)
diff --git a/model_server/base/roiset.py b/model_server/base/roiset.py
index f624460f..9f7de716 100644
--- a/model_server/base/roiset.py
+++ b/model_server/base/roiset.py
@@ -1,7 +1,7 @@
import itertools
from math import sqrt, floor
from pathlib import Path
-from typing import List, Union
+from typing import Dict, List, Union
from typing_extensions import Self
from uuid import uuid4
@@ -386,12 +386,17 @@ class RoiSet(object):
@staticmethod
def from_bounding_boxes(
acc_raw: GenericImageDataAccessor,
- bbox_df: pd.DataFrame,
+ bbox_yxhw: List[Dict],
+ bbox_zi: Union[List[int], int] = None,
params: RoiSetMetaParams = RoiSetMetaParams()
):
+ bbox_df = pd.DataFrame(bbox_yxhw)
+ if list(bbox_df.columns.str.upper().sort_values()) != ['H', 'W', 'X', 'Y']:
+ raise BoundingBoxError(f'Expecting bounding box coordinates Y, X, H, and W, not {list(bbox_df.columns)}')
- # deproject if zi is not provided
- if 'zi' not in bbox_df.columns:
+
+ # deproject if zi is not specified
+ if bbox_zi is None:
def _slice_zmax(r):
acc_raw.crop_hw(
r.y0,
@@ -400,7 +405,8 @@ class RoiSet(object):
r.x1 - r.x0
)
zmax = acc_raw.data.argmax(axis=3, keepdims=True)[:, :, 0, 0].astype('uint16')
- bbox_df['zi'] = 0
+ else:
+ bbox_df['zi'] = bbox_zi
df = df_insert_slices(
bbox_df,
@@ -1010,6 +1016,9 @@ class RoiSet(object):
class Error(Exception):
pass
+class BoundingBoxError(Error):
+ pass
+
class DeserializeRoiSet(Error):
pass
diff --git a/tests/base/test_roiset.py b/tests/base/test_roiset.py
index afc75f35..ba553564 100644
--- a/tests/base/test_roiset.py
+++ b/tests/base/test_roiset.py
@@ -626,6 +626,14 @@ class TestRoiSetSerialization(unittest.TestCase):
self.assertTrue(ref_roiset.contains_segmentation)
self.assertTrue(ref_roiset.contains_segmentation)
+class TestRoiSetObjectDetection(unittest.TestCase):
+
+ def setUp(self) -> None:
+ # set up test raw data and segmentation from file
+ self.stack = generate_file_accessor(data['multichannel_zstack_raw']['path'])
+ self.stack_ch_pa = self.stack.get_mono(params['segmentation_channel'])
+ self.seg_mask_3d = generate_file_accessor(data['multichannel_zstack_mask3d']['path'])
+
def test_create_roiset_from_bounding_boxes(self):
from skimage.measure import label, regionprops, regionprops_table
--
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